PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os05g03040.2
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family AP2
Protein Properties Length: 362aa    MW: 40079.9 Da    PI: 7.1519
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os05g03040.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP2544e-17170219155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkr.krfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV++++++grW+++I+d      + k+++lg f+ta  Aa+a+++a+ k++g
  LOC_Os05g03040.2 170 SQYRGVTFYRRTGRWESHIWD------CgKQVYLGGFDTAHAAARAYDRAAIKFRG 219
                       78*******************......55************************997 PP
2AP230.49.9e-10262303146
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaa 46 
                       s+y+GV+ +k  grW+A+   +     +k+++lg f+++ eAa++ 
  LOC_Os05g03040.2 262 SKYRGVTLHK-CGRWEARMGQF--L-GKKYIYLGLFDSEVEAARLS 303
                       89********.7******5553..2.26**********99***986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541715.17E-16170228IPR016177DNA-binding domain
PfamPF008473.7E-9170219IPR001471AP2/ERF domain
CDDcd000182.32E-11171229No hitNo description
SMARTSM003802.4E-32171233IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.102.2E-17171228IPR001471AP2/ERF domain
PROSITE profilePS5103217.596171227IPR001471AP2/ERF domain
SuperFamilySSF541715.56E-9262303IPR016177DNA-binding domain
CDDcd000183.32E-13262301No hitNo description
PfamPF008471.3E-5262304IPR001471AP2/ERF domain
SMARTSM003801.0E-6263318IPR001471AP2/ERF domain
PROSITE profilePS510328.913263301IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.101.6E-5263301IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 362 aa     Download sequence    Send to blast
MELDLNNVAE GVVEKHETAA RSDSGTSESS VLNGEASGAA IAPAEEGSSS TPPSPPPPPA  60
AVLEFSILRS SASASGENDA DDDEEEEATP SPPPHHQHQQ LLVTRELFPS AAPSPQHWAE  120
LGFLRPDPPR PHPDIRILAH APPPAPPPPP PQPQPQAAKK SRRGPRSRSS QYRGVTFYRR  180
TGRWESHIWD CGKQVYLGGF DTAHAAARAY DRAAIKFRGV EADINFNLSD YEEDMRQMKS  240
LSKEEFVHVL RRQSTGFSRG SSKYRGVTLH KCGRWEARMG QFLGKKYIYL GLFDSEVEAA  300
RLSSAWILFS CTIDSNQKKV FSFLKFYFLV LLIFDGPCTD SNLLSFFFSS FFSSRFKHQG  360
L*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.616450.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Accumulates progressively in panicles. Present at low levels in developing seeds, with a progressive decrease during development (PubMed:20713616). In spikelets, fades out progressively after anthesis (PubMed:25817414). {ECO:0000269|PubMed:20713616, ECO:0000269|PubMed:25817414}.
UniprotTISSUE SPECIFICITY: Mostly expressed in roots, seedlings and leaves and, to a lower extent, in stems, panicles and developing seeds (PubMed:20713616). Present in spikelets (PubMed:25817414). {ECO:0000269|PubMed:20713616, ECO:0000269|PubMed:25817414}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor (By similarity). Involved in spikelet transition (Probable). Regulator of starch biosynthesis especially during seed development (e.g. endosperm starch granules); represses the expression of type I starch synthesis genes (PubMed:20713616). Prevents lemma and palea elongation as well as grain growth (PubMed:28066457). {ECO:0000250|UniProtKB:P47927, ECO:0000269|PubMed:20713616, ECO:0000269|PubMed:28066457, ECO:0000305|PubMed:26631749}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00615PBMTransfer from AT2G28550Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os05g03040.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Target of miR172 microRNA mediated cleavage, particularly during floral organ development (Probable). Repressed by SRT1 via epigenetic histone H3K9 acetylation (H3K9ac) regulation (PubMed:27181944). {ECO:0000269|PubMed:27181944, ECO:0000305|PubMed:26631749, ECO:0000305|PubMed:28066457}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs05g03040
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6851170.0AY685117.1 Oryza sativa (japonica cultivar-group) transcription factor AP2D23-like (AP2D23) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015639329.10.0AP2-like ethylene-responsive transcription factor TOE3 isoform X1
SwissprotQ2TQ340.0AP21_ORYSJ; APETALA2-like protein 1
TrEMBLA0A0E0PGU60.0A0A0E0PGU6_ORYRU; Uncharacterized protein
TrEMBLA0A0E0PGU70.0A0A0E0PGU7_ORYRU; Uncharacterized protein
STRINGOS05T0121600-010.0(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G28550.39e-77related to AP2.7
Publications ? help Back to Top
  1. Fu FF,Xue HW
    Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator.
    Plant Physiol., 2010. 154(2): p. 927-38
    [PMID:20713616]
  2. Sekhar S, et al.
    Spikelet-specific variation in ethylene production and constitutive expression of ethylene receptors and signal transducers during grain filling of compact- and lax-panicle rice (Oryza sativa) cultivars.
    J. Plant Physiol., 2015. 179: p. 21-34
    [PMID:25817414]
  3. Wang L, et al.
    Coordinated regulation of vegetative and reproductive branching in rice.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(50): p. 15504-9
    [PMID:26631749]
  4. Zhang H,Lu Y,Zhao Y,Zhou DX
    OsSRT1 is involved in rice seed development through regulation of starch metabolism gene expression.
    Plant Sci., 2016. 248: p. 28-36
    [PMID:27181944]
  5. Dai Z,Wang J,Zhu M,Miao X,Shi Z
    OsMADS1 Represses microRNA172 in Elongation of Palea/Lemma Development in Rice.
    Front Plant Sci, 2016. 7: p. 1891
    [PMID:28066457]